get_mut_trinuc_strand: Derive quadnucleotide contexts, strandedness and single-base...

In reimandlab/RM2: Regression Models For Localised Mutations

Derive quadnucleotide contexts, strandedness and single-base substitutions

Description

get_mut_trinuc_strand() takes a data frame of mutations and determines the quadnucleotide context (trinucleotide context + alternate allele) and strand.

Usage

get_mut_trinuc_strand(maf)

Arguments

maf

Data frame of mutations with the following columns: chr, start, end, ref and alt chr autosomal chromosomes as chr1 to chr22 and sex chromosomes as chrX and chrY start the start position of the mutation in base 1 coordinates end the end position of the mutation in base 1 coordinates ref the reference allele as a string containing the bases A, T, C or G alt the alternate allele as a string containing the bases A, T, C or G

Value

Data frame containing additional mutation context columns

chr

autosomal chromosomes as chr1 to chr22 and sex chromosomes as chrX and chrY

start

the start position of the mutation in base 1 coordinates

end

the end position of the mutation in base 1 coordinates

ref

the reference allele as a string containing the bases A, T, C or G

alt

the alternate allele as a string containing the bases A, T, C or G

mut_trinuc

pyrimidine-centered quadnucleotide mutation context and indel

mut_strand

the mutation strand classified as w for Watson and c for Crick

ref_alt

pyrimidine single-base substitution

reimandlab/RM2 documentation built on Aug. 13, 2022, 12:22 p.m.